Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3298
  Reference Plasmid   MGYG000298113__MGYG000298113_12
  Reference Plasmid Size   40387
  Reference Plasmid GC Content   0.58
  Reference Plasmid Mobility Type   non-mobilizable





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0134260 LFJNNBDC_00028 30267 3 Oral 1.00 protein_coding synonymous_variant LOW 96G>T Leu32Leu
M0134261 LFJNNBDC_00028 30276 3 Oral 1.00 protein_coding synonymous_variant LOW 105T>C Tyr35Tyr
M0134262 LFJNNBDC_00028 30289 3 Oral 1.00 protein_coding missense_variant MODERATE 118G>A Val40Ile
M0134263 LFJNNBDC_00028 30300 3 Oral 1.00 protein_coding synonymous_variant LOW 129G>A Arg43Arg
M0134264 LFJNNBDC_00028 30346 3 Oral 1.00 protein_coding missense_variant MODERATE 175A>G Asn59Asp
M0134265 LFJNNBDC_00028 30351 3 Oral 1.00 protein_coding synonymous_variant LOW 180G>C Ala60Ala
M0134266 LFJNNBDC_00028 30381 3 Oral 1.00 protein_coding synonymous_variant LOW 210T>C Leu70Leu
M0134267 LFJNNBDC_00028 30591 3 Oral 1.00 protein_coding missense_variant MODERATE 420C>G His140Gln
M0134268 LFJNNBDC_00028 30692 3 Oral 1.00 protein_coding missense_variant MODERATE 521T>G Leu174Arg
M0134269 LFJNNBDC_00028 30693 3 Oral 1.00 protein_coding synonymous_variant LOW 522T>C Leu174Leu
M0134270 LFJNNBDC_00029 30952 3 Oral 1.00 protein_coding missense_variant MODERATE 51A>C Gln17His
M0134271 LFJNNBDC_00030 31747 3 Oral 1.00 protein_coding missense_variant MODERATE 394G>A Gly132Ser
M0134272 LFJNNBDC_00030 31799 3 Oral 1.00 protein_coding missense_variant MODERATE 446C>G Ala149Gly
M0134273 LFJNNBDC_00030 31917 3 Oral 1.00 protein_coding synonymous_variant LOW 564T>C Leu188Leu
M0134274 LFJNNBDC_00030 32043 3 Oral 1.00 protein_coding synonymous_variant LOW 690G>A Arg230Arg
M0134275 LFJNNBDC_00030 32130 3 Oral 1.00 protein_coding synonymous_variant LOW 777T>C Val259Val
M0134276 LFJNNBDC_00030 32227 3 Oral 1.00 protein_coding missense_variant MODERATE 874T>C Ser292Pro
M0134277 LFJNNBDC_00030 32228 3 Oral 1.00 protein_coding missense_variant MODERATE 875C>A Ser292Tyr
M0134278 LFJNNBDC_00030 32664 3 Oral 1.00 protein_coding synonymous_variant LOW 1311A>C Val437Val
M0134279 LFJNNBDC_00030 32777 3 Oral 1.00 protein_coding missense_variant MODERATE 1424A>C Lys475Thr
M0134280 LFJNNBDC_00030 32859 3 Oral 1.00 protein_coding synonymous_variant LOW 1506A>G Glu502Glu
M0134281 LFJNNBDC_00030 33135 3 Oral 1.00 protein_coding synonymous_variant LOW 1782A>G Gly594Gly
M0134282 LFJNNBDC_00030 33162 3 Oral 1.00 protein_coding synonymous_variant LOW 1809T>C Tyr603Tyr
M0134283 LFJNNBDC_00030 33292 3 Oral 1.00 protein_coding missense_variant MODERATE 1939G>T Ala647Ser
M0134284 LFJNNBDC_00030 34268 3 Oral 1.00 protein_coding missense_variant MODERATE 2915A>C Glu972Ala
M0134285 LFJNNBDC_00030 34271 3 Oral 1.00 protein_coding splice_region_variant&stop_retained_variant LOW 2918A>G Ter973Ter






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term